Research workbench
D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7-bisphosphatase of synechocystis sp. pcc 6803 in complex with fructose-1,6- bisphosphate
Analyse D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7-bisphosphatase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RPL
- Type
- protein
- Length
- 1,389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase
- EC
- 3.1.3.11, 3.1.3.37
- UniProt
- P73922
- Ligands
- FBP, AMP, MG, SO4, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 347 | 33% helix, 27% strand | P73922 |
| B | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 349 | 32% helix, 28% strand | P73922 |
| D | D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE 1,7- bisphosphatase (EC 3.1.3.11, 3.1.3.37) | protein | 346 | 32% helix, 27% strand | P73922 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.85 | 0.86 | 121 | AMP, CL |
| 2 | 811 | 0.83 | 0.86 | 91 | empty |
| 3 | 508 | 0.77 | 0.84 | 55 | AMP |
| 4 | 175 | 0.58 | 0.82 | 42 | empty |
| 5 | 278 | 0.55 | 0.77 | 36 | MG, FBP |
Interfaces
6 interfaces between chains.
- B–C · 1679 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1648 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1372 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 3RPL · D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis… · the same entry in another collection · chain D against D, TM-score 1.00
- P73922 · AlphaFold monomer V2.0 prediction for D-fructose 1,6-bisphosphatase class 2/SEDOHEPTULOSE… · a predicted model of the same protein · chain D against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P73922
- Elsewhere: RCSB PDB 3RPL · PDBe 3RPL · UniProt P73922
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